TABLE 1.

Genome features of “Ca. Nitrosotenuis aquarius” and selected Thaumarchaeota representatives

Genome feature	Value for the parametera
	“Ca. Nitrosotenuis aquarius” AQ6F	“Ca. Nitrosotenuis uzonensis” N4	“Ca. Nitrosotenuis cloacae” SAT1	“Ca. Nitrosoarchaeum limnia” BG20	“Ca. Nitrosopumilus maritimus” SCM1	“Ca. Nitrosotalea devanaterra” Nd1	Nitrososphaera viennensis EN76	“Ca. Nitrosocosmicus exaquare” G61
Cluster	I.1a	I.1a	I.1a	I.1a	I.1a	I.1a-associated	I.1b	I.1b
Habitat	Freshwater aquarium	Hot spring	WWTP	Estuary	Marine aquarium	Acidic soil	Garden soil	WWTP
Genome size (Mb)	1.70	1.65	1.62	1.86	1.65	1.81	2.53	2.99
GC content (%)	42.2	42.3	41.0	32.5	34.2	37.1	52.7	33.9
Total no. of genomic objects	2,088	1,999	1,955	2,632	2,012	2,144	3,267	3,391
No. of protein-coding genes	2,047	1,958	1,911	2,589	1,976	2,106	3,128	3,354
Coding density (%)	92.2	90.4	91.9	87.2	91.7	90.6	86.4	77.1
5S rRNA copy no.	1	1	1	1	1	1	1	1
16S/23S rRNA copy no.	1	1	1	1	1	1	1	2
No. of tRNAs	38	38	40	38	40	37	39	39
amoA copy no.	1	1	1	1	1	1	1	1
amoB copy no.	1	1	1	1	1	1	1	1
amoC copy no.	1	1	1	1	1	1	1	3
Nitrite reductase (nirK)	+	+	+	+	+	+	+	+
No. of ammonium transporters	2	2	2	2	2	3	3	1
Urease and accessory proteins	+	−	+	−	−	−	+	+
Urea transporters	−	−	+c	−	−	−	+	+
Carbon fixation	3HP/4HB	3HP/4HB	3HP/4HB	3HP/4HB	3HP/4HB	3HP/4HB	3HP/4HB	3HP/4HB
Flagellar proteins	+	+	+	+	−	+	+	−
Chemotaxis proteins	+	+	+	+	−	+	+	−
S-layer-associated proteins	+	+	+	+	+	+	+	−
Coenzyme F420	+	+	+	+	+	+	+	+
Cobalamin synthesis	+	+	+	+	+	+	+	+
Short-chain PHA synthesis (phaC or phaE)b	+	+	+	+	+	+	+	+
Dicarboxylate transporter (SdcS)	+	+	−	−	+	−	−	+
Citrate transporter	+	−	−	+	−	−	−	−
Amino acid/oligopeptide transport	+	+	+	+	+	+	+	+
Reference	This work	19	24	17	102	44	22	39

^aPlus and minus signs indicate presence and absence, respectively.

^bPHA, polyhydroxyalkanoic acid.

^cTruncated transporter.